Protein Structure Analysis, Comparison &/or Classification :

• CATH : Home Page. Protein Structural Classification. Biomolecular Structure and Modelling Unit. University College London.
• COMPARER : Comparer On-Line. Protein structural comparison technique which operate simultaneously at several levels in the hierarchy of the protein structure. At each level, the features compared are properties or relationships. A. Sali & T.L. Blundell, 1990.
• DALI Server : Home Page. EMBL Network Service for comparing protein structures in 3D.
• DDD : Dali Domain Dictionary is a structural clasification of protein domains. Domains are delineated automatically optimising topological recurrence between large, compact units in the know protein structures.
• 3-Dee : Database of Protein Domain Definitions. This database contains definitions of structural domains for all protein chains in the Brookhaven Protein Databank that have 20 or more residues and are not theorical models.
• FSSP : FSSP Home Page. Fold Classification based on Structure-Structure Alignment of proteins. L. Holm and C. Sander.
• MolMovDB : Database of Macromolecular Movements with Associated Tools for Geometric Analysis. M. Gerstein.
• PQS : A Quaternary Structure File Server. Internet resource that makes avaible coordinates for likely quaternary states for structures contained in the PDB that were determined by X-ray crystallography. The EBI MSD Group.
• PROCHECK : Home Page. Procheck checks the stereochemical quality of a protein structure, producing a number of Postcript plots analysing its overal and residue-by-residue geometry.
• PROMOTIF : A suite of programs to analyse structural motifs. Promotif analyses a protein coordinate file and provides details of the strucutral motifs in the protein.
• SARF2 : Spatial ARrangement of backbone Fragments. Fast Detection of Topological and Nontopological Structural similarities in the PDB. N.N. Alexandrov & D. Fischer.
• SAS : Sequences Annoted by Structure. A tool to apply structural information to protein sequences. SAS is a tool which aims to bridge the gap between protein sequence and structural analysis, and aid identification of a protein sequence, by using structural information to recognise distant homologues.
• SCOP : Home Page A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. MRC Laboratory of Molecular Biology and Centre of Protein Engineering. Hills Road, Cambridge, UK.
• STAMP : Structural Alignment of Multiple Proteins. It provides not only multiple alignments and the corresponding ībest-fit` superpositions, but also a systematic and reproducible method for assesing the quality of such alignments. R.B. Russel & G.J. Barton.
• STING : Sequence To and withIN Graphics. WWW tool for simultaneus display of information about macromolecular structure and sequence. Special attention is given to macromolecular interface analysis.
• VAST : Vector Alignment Search Tool. An algorithm that identifies significantly similar 3-dimensional substructures.
  

Ingeborg M.M. van Leeuwen
ingeborg@goliat.ugr.es